EES 4760/5760: Agent- and Individual-Based Computational Modeling on EES 4760/5760

Set up NetLogo

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Preliminary Information

There is nothing for you to turn in, but do the following task to prepare for next week:

Homework Exercises:

Download NetLogo version 6.4.0 from https://ccl.northwestern.edu/netlogo/ and install it on your computer.

Introducing NetLogo

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

As you read along with Section 2.3, follow along on your computer and build the Mushroom Hunt model by typing in the code shown in the textbook. The whole program is shown on pages 27–29. Save your model as mushroom_hunt.nlogo.

This exercise may seem very simple, but it is the first step toward learning how to program NetLogo and it will be an important first step toward writing your own models.

The computer modeling cycle

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

Required Reading (everyone):

Agent-Based and Individual-Based Modeling, Ch. 1.
Handout: P. Tyson, “Artificial Societies,” Technology Review 100 (3), 15–17 (1997)..

Optional Extra Reading:

Modeling Social Behavior, Ch. 1.

Reading Notes:

This reading sets the stage for answering the questions:

What is computational modeling and why is it useful in social and natural science research?
What are agent based models? How are they different from other kinds of models? What makes them useful for scientific research?

The reading introduces the idea of a modeling cycle. You should understand the different steps in the modeling cycle. You should also think about why Railsback and Grimm describe modeling as a cycle, as opposed to a linear process with a start and stop.

Becoming familiar with NetLogo

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Preliminary Information

This homework consists of reading and working through tutorials, so there is nothing to turn in.

Homework Exercises:

Everyone should do exercises 2.1 and 2.2 in Chapter 2 of Railsback & Grimm. This consists of reading and working through tutorials, so there is nothing to turn in.

Introduction to NetLogo

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

Required Reading (everyone):

Agent-Based and Individual-Based Modeling, Ch. 2.

Optional Extra Reading:

Modeling Social Behavior, Ch. 2.

Reading Notes:

Familiarize yourself with NetLogo. I recommend that you read through the chapter with NetLogo open on your computer. Feel free to play around with NetLogo and try things out. The homework consists of following the step-by-step creation of a model in section 2.3.

The chapter from Modeling Social Behavior is purely optional. You don’t need to read it, and everything you need to know is covered in the reading from Railsback & Grimm, but it may be interesting to read this alternate introduction to the NetLogo modeling system and programming language.

Experimenting with NetLogo

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Preliminary Information

Upload your work to Brightspace when you’re done (Word or text files for the descriptions and ODD document, and .nlogo files for your NetLogo models).

When there is more than one file for a homework assignment, I recommend that you make a Zip file containing all of the files for the different parts of the assignment and upload the Zip file to Brighspace instead of uploading the files separately. When a homework assignment has more than one problem, and each problem has multiple files, it can be helpful to have a separate folder for each problem, and put all of these folders into the ZIP file that you turn in.

Specifying models: The ODD protocol

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

Required Reading (everyone):

Agent-Based and Individual-Based Modeling, Ch. 3.

Reading Notes:

Read carefully through the different design principles. Some of them have meanings that are a bit different from what you might infer from colloquial use.

For instance:

Adaptation does not mean a persistent change in a turtle’s behavior similar to the biological/Darwinian sense of adaptation in species. Rather, it means the way an agent changes its behavior in response to its immediate conditions. Thus, adaptation in the ODD sense might include behaviors such as eating when you are hungry (eating is an adaptation to hunger), putting on warmer clothing when it’s cold out (bundling up is an adaptation to cold), and running away from a predator.
The kind of persistent changes that arise over time from experience fall under the ODD design concept of learning: If there is more food near a river than on hills, turtles may learn to go to rivers when they are hungry.

You can download several useful documents related to the ODD protocol from the class web site:

Science with models: Butterfly mating

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Preliminary Information

Some problems in this homework set call for you to write a NetLogo model and also answer questions about the model. For answering the questions, you may take any of these approaches:

Edit the INFO page for your NetLogo model and add the following (this example is for exercise 5.4)
```
# Exercise 5.4

When I ran the model ...
```
Write your answer in a Word file or other document file (text, PDF, etc.) with the title homework_answers.docx and put the homework answers in there, as follows:

Your first model

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

Required Reading (everyone):

Agent-Based and Individual-Based Modeling, Ch. 4.

Reading Notes:

For the reading, read Chapter 4 in Agent-Based Modeling first and focus mostly on this chapter.

It is worth noting that the Sugarscape model you read about for Aug. 25 is very similar to the hilltopping model. Sugarscape was part of a very influential research project in the 1990s, in which Joshua Epstein and Robert Axtell showed that a very simple model could reproduce complex biological and economic phenomena that are observed in real societies and ecosystems. You may find it interesting at this point to look back at the “Artificial Societies” article and to play with the Sugarscape model in NetLogo.

Reproducing a model from its ODD

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

Graduate Students:
- Graduate students should do Railsback & Grimm, Ex. 5.11

Notes on Homework:

Graduate Students: You can download the journal article for this exercise, R. Jovani & V. Grimm. (2008) “Breeding synchrony in colonial birds: From local stress to global harmony”, Proc. Royal Soc. London B 275, 1567–63 from the class web site, https://ees4760.jmgilligan.org/files/models/chapter_05/Jovani_Grimm_2008_Breeding.pdf.

You don’t have to reproduce all of the figures in the paper. Focus on reproducing the information in Figure 2 (make a figure of colony synchrony versus NR and some other figures showing histograms of breeding dates for NR = 0.00, 0.08, 0.20, and 1.00 and comparing them to the histograms in Fig. 2.

Using models for science

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

Required Reading (everyone):

Agent-Based and Individual-Based Modeling, Ch. 5.

Optional Extra Reading:

Modeling Social Behavior, Ch. 3.

Reading Notes:

This reading sets the stage for answering the big question, “How can we use agent-based models to do science?” There are several aspects to this question, which this chapter will introduce:

How can we produce quantitative output from our models?
How can your models read and write data to and from files? (This is important for connecting your model to other parts of your project)
How should we test our models to make sure they do what we think they do? (More on this in Chapter 6)
Making your research reproducible by using version control and documentation.

A number of you may like to use Excel or statistical analysis tools, such as R, SPSS, or Stata. The material in this chapter about importing and exporting data using text or .csv files will be very useful for this. By default, NetLogo only allows you to read in data in simple text files. However, if comes with some extensions that you can use to read in data from other common file formats, including .csv and ArcGIS shapefiles and raster (grid) files.

Research project proposal

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

Turn in a one-to-two page (double-spaced) proposal for your semester research project.

Notes on Homework:

This proposal should describe the topic you want to work on, identify a published open-source model you want to work with, and and describe how you think you might want to extend it.

You should consult the textbook, the Model Library in NetLogo, and the list of reading and computational tools and resources I distributed on the first day of class (it’s also posted on the course web site).

Testing and validating models

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

Required Reading (everyone):

Agent-Based and Individual-Based Modeling, Ch. 6.

Reading Notes:

No one writes perfect programs. Errors in programs controlling medical equipment have killed people. Errors in computer models and data analysis code have not had such dire results, but have wasted lots of time for researchers and have caused public policy to proceed on incorrect assumptions. In many cases, these errors were uncovered only after a great deal of frustration because the original researchers would not share their computer codes with others who were suspicious of their results.

Testing and debugging

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

Everyone:
- Railsback & Grimm, Ch. 6, Ex. 6.2, 6.3
Graduate Students, also do the following:
- Railsback & Grimm, Ch. 6, Ex. 6.4, 6.5

Notes on Homework:

You do not need to turn anything in for Exercise 6.2. This is an exercise to try for the experience

A hint for exercise 6.3: Patches have integer coordinates (representing the center of the patch). How does the turtle determine the angle to face during setup? How does it determine the angle to face in go-back? Can you think of a different way to record the path so the go-back exactly retraces the path it took during setup? If you knew the direction the turtle was heading at each step during setup, could you use this heading information to exactly retrace the path?

Choosing Research Projects

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

Required Reading (everyone):

Agent-Based and Individual-Based Modeling, Ch. 7.

Reading Notes:

There is not very much reading for today. Read Chapter 7 of Agent-Based Modeling carefully (it’s very short) The point of this chapter is to help you get ideas for your term research project.

Before class, I want you to read through the research project assignment and think about what you might want to do for a research project. We will spend class talking about possible research projects.

Analyzing model experiments

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

Everyone:
- Railsback & Grimm, Ch. 8, Ex. 8.1, 8.2
- Railsback & Grimm, Ch. 9, Ex. 9.3, 9.4
Graduate Students, also do the following:
- Railsback & Grimm, Ch. 8, Ex. 8.3, 8.4
- Railsback & Grimm, Ch. 9, Ex. 9.6

Emergence

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

Required Reading (everyone):

Agent-Based and Individual-Based Modeling, Ch. 8.

Reading Notes:

This is a major chapter. Emergence is one of the most important concepts in agent-based modeling, so pay close attention to the discussion in this chapter and think about how you can measure and assess emergence.

This chapter also introduces a very important tool for doing experiments in NetLogo: BehaviorSpace. BehaviorSpace lets you repeatedly run a NetLogo model while varying the settings of any of the controls on your user interface. Where there is randomness (stochasticity) in the model, you can perform many runs at each set of control settings. This will let us perform sensitivity analysis to determine whether a certain emergent phenomenon we are investigating happens only for values of the parameters within a narrow range, or whether it happens over a wide range of the parameters. It will let us determine which parameters are most important for the phenomenon.

Programming agent sensing

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

Optional: The following exercises are optional. You can turn them in for extra credit.

Railsback & Grimm, Ch. 10, Ex. 10.1
Railsback & Grimm, Ch. 11, Ex. 11.1

Observation

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

Required Reading (everyone):

Agent-Based and Individual-Based Modeling, Ch. 9.

Reading Notes:

In this chapter, we examine how to detect and record the properties of a model that we want to study.

The article, D. Kornhauser, U. Wilensky, and W. Rand. (2009). “Design guidelines for agent-based model visualization,” Journal of Artificial Societies and Social Simulation 12, 1 is available online at https://jasss.soc.surrey.ac.uk/12/2/1.html.

I have posted a refresher guide for NetLogo programming on the class web site at https://ees4760.jmgilligan.org/files/models/chapter_09/ch9_ex8_netlogo_exercises.pdf

Resources

Wed, 22 Aug 2018 00:00:00 +0000

Team modeling project presentations

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

Teams will give a presentation on their projects.

Notes on Homework:

See the team project assignment sheet for details on what I expect for the presentation.

Sensing

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

Required Reading (everyone):

Agent-Based and Individual-Based Modeling, Ch. 10.

Reading Notes:

In addition to the assigned reading from the textbook, read the ODD for your team project before you come to class. The ODDs are posted on Brightspace and the class web site.

For some of the class period, you and your team will start translating the ODD for your project model into NetLogo code.

Important programming concepts in this chapter include:

Research project model analysis

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

Study the code and ODD of the model you chose for your semester research project, play with the model and run some BehaviorSpace experiments to examine its output.

Turn in a 3–5 page (double-spaced) write-up about the model.

Notes on Homework:

See the project assignment sheet for details about this assignment.

Adaptive Behavior and Objectives

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

Required Reading (everyone):

Agent-Based and Individual-Based Modeling, Ch. 11.

Reading Notes:

Agents’ behavior often consists of trying to achieve some objective.

I have discussed the way that Adam Smith’s “invisible hand of the market” is a kind of agent-based view of a nation’s economy: Each person (agent) has an objective of trying to maximize his or her own wealth (that’s the agent’s micromotive), and in doing so, the population of agents manages unintentionally to maximize the total wealth of the nation (an emergent macrobehavior that results from the collective interactions of the agents and their micromotives).

Team modeling project report

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

Turn in the written report for your team project on Brightspace.

Notes on Homework:

See the team project assignment sheet for details.

Prediction

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

Required Reading (everyone):

Agent-Based and Individual-Based Modeling, Ch. 12.

Reading Notes:

In class, we will discuss the telemarketer model.

For the teams working on the telemarketer model, the steps are:

Build the model as described in the ODD.
Do the analyses in section 13.3.2
Next work on two extensions:
1. Mergers (section 13.5)
2. Customers remember (section 13.6)

Before class, everyone should read Chapter 13 and the ODD for the telemarketer model and be ready to discuss the model in class. This will be a chance for the teams working on the model to ask questions.

Research project ODD

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

Turn in an ODD for extending your chosen model to ask new questions.

Notes on Homework:

See the semester research project assignment sheet for details.

Interaction

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

Required Reading (everyone):

Agent-Based and Individual-Based Modeling, Ch. 13.

Optional Extra Reading:

Modeling Social Behavior, Ch. 6–7, 9.

Reading Notes:

The optional reading from Modeling Social Behavior may be interesting. Chapters 6–7 apply agent-based modeling to game-theory and chapter 9 looks into social networks among agents in detail.

Chapter 6 focuses on a class of strategic games, such as the Prisoner’s Dilemma, in which the players do better when they cooperate with each other, but the game gives each player has a strong temptation to betray their partner. The chapter investigates a rich line of research, which shows that there may be reasons for natural selection to favor cooperation, so people may have evolved to be mostly trustworthy and cooperative.

Draft model code for research project

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

Turn in a draft .nlogo file with your modified model. The ODD for your modified model should be included in the “Info” section of the model.

You should also turn in a document that describes what you are satisfied with about your draft model and what problems you are struggling with.

Notes on Homework:

The model code you turn in should run, but it does not need to be perfect.

Team Presentations

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

No new reading for today.

Notes:

There is no reading for today. You will do your team project presentations in class.

Research project presentation

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

You will make a five-minute presentation in class about your model (You can use the full five minutes of talking and there will be an additional two minutes for questions).

Notes on Homework:

There will not be time to go into all the details in your presentation, so focus on:

Structure:

Start by describing your research question
Briefly describe your model
Describe the experiments you performed:
- What outputs did you observe or measure?
- What parameters did you change?
- What did you see? (e.g., behaviorspace graphs or screenshots of the model)
Conclusions

General recommendations:

5 slides, one minute each.
As much as you can, use figures (graphs, illustrations, images, etc.) instead of text.
Avoid slides with a lot of text

You can’t say everything you did, so focus on the most interesting highlights.

Research Project ODDs

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

No new reading for today.

Notes:

There is no reading for today. We will spend class discussing your individual projects and your work on creating an ODD for your model.

Research project presentation

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

You will make a five-minute presentation in class about your model (You can use the full five minutes of talking and there will be an additional two minutes for questions).

Notes on Homework:

There will not be time to go into all the details in your presentation, so focus on:

Structure:

Start by describing your research question
Briefly describe your model
Describe the experiments you performed:
- What outputs did you observe or measure?
- What parameters did you change?
- What did you see? (e.g., behaviorspace graphs or screenshots of the model)
Conclusions

General recommendations:

5 slides, one minute each.
As much as you can, use figures (graphs, illustrations, images, etc.) instead of text.
Avoid slides with a lot of text

You can’t say everything you did, so focus on the most interesting highlights.

Scheduling

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

Required Reading (everyone):

Agent-Based and Individual-Based Modeling, Ch. 14.

Reading Notes:

A good example of asynchronous updating is the model of breeding synchrony, described in Jovani and Grimm (2008) and in Chapter 23, which I have posted on the class web site: https://ees4760.jmgilligan.org/files/models/chapter_23/Ch_23_4_breeding_synchrony.nlogo

Research project report

Thu, 31 Jul 2025 00:00:00 +0000

Homework

Homework Exercises:

Turn in a written report about your research project. Your report should follow the model of a research report for Science magazine:

Notes on Homework:

Your report should have the following structure:

Abstract (1 paragraph summary of the paper, focusing on highlights)
Introduction
- Research question and why it’s interesting
Methods
- Describe the model you started with and how you changed it to answer your research question
- Describe the experiments you ran with the model.
- Describe what outputs you measured
Results
- What did you see (graphs of output, pictures of turtles on patches, etc.)
Discussion, conclusions:
- What did you learn from the results of your experiment?
- If you had more time, what would you do next with your model?
- Do you think these results point to possible uses for your model?
References

See the assignment for further details.

Stochasticity

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

Required Reading (everyone):

Agent-Based and Individual-Based Modeling, Ch. 15.

Collectives

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

Required Reading (everyone):

Agent-Based and Individual-Based Modeling, Ch. 16.

Patterns

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

Required Reading (everyone):

Agent-Based and Individual-Based Modeling, Ch. 17–18.

Reading Notes:

You can download the ODD for the BEFORE beech forest model, which is described in section 18.3, from the class web site: https://ees4760.jmgilligan.org/files/models/chapter_18/ch18_before_ODD.pdf.

I have also posted a list of published models in which observed patterns are important: https://ees4760.jmgilligan.org/files/models/chapter_18/ch18_ex1_models_list.pdf

Artificial Societies

Thu, 22 Aug 2019 00:00:00 +0000

Reading for Aug. 25

Peter Tyson, “Artificial Societies ,” MIT Technology Review 100(3), 15–17 (Apr., 1997). https://www.ees4760.jmgilligan.org/files/reading/Tyson_Artificial_Societies_1997.pdf

Theory Development

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

Required Reading (everyone):

Agent-Based and Individual-Based Modeling, Ch. 19.

Optional Extra Reading:

Modeling Social Behavior, Ch. 8.

Reading Notes:

There is an implementation of the wood hoopoe model, suitable for Exercise 2, on the class web site: https://ees4760.jmgilligan.org/files/models/chapter_19/ch19_ex2_wood_hoopoes.nlogo

The optional chapter from Modeling Social Behavior discusses other approaches to using agent-based models to do science. The readings from Railsback & Grimm focus on the methodology of Pattern-Oriented Modeling. This chapter looks at other ways of thinking about connecting agent-basedm models to scientific methods. The focus here is on statistical analysis of experimental results and the use of Bayesian statistical methods to identify and avoid pitfalls where experiemnts may fool researchers into drawing the wrong conclusion (e.g., thinking a hypothesis is true, when it’s really false).

Parameterization and Calibration

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

Required Reading (everyone):

Agent-Based and Individual-Based Modeling, Ch. 20.

Agent-Based Models in Practice

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

No new reading for today.

Analyzing ABMs

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

Required Reading (everyone):

Agent-Based and Individual-Based Modeling, Ch. 22.

Sensitivity and Robustness

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

Required Reading (everyone):

Agent-Based and Individual-Based Modeling, Ch. 23.

Reading Notes:

You can download the model of breeding synchrony, described in Jovani and Grimm (2008) and in section 23.4, from the class web site: https://ees4760.jmgilligan.org/files/models/chapter_23/Ch_23_4_breeding_synchrony.nlogo

Looking Ahead: ABMs Beyond this Course

Thu, 31 Jul 2025 00:00:00 +0000

Reading:

Required Reading (everyone):

Agent-Based and Individual-Based Modeling, Ch. 24.

Optional Extra Reading:

Modeling Social Behavior, Ch. 10–11.

Reading Notes:

The optional reading from Modeling Social Behavior provides perspectives on the relationship between simulation models and the real world and how to use models wisely by appreciating both what they can do and what they can’t do, what parts of the real world they capture faithfully and which parts they don’t.

Sugarscape Model from Class #3

Thu, 22 Aug 2019 00:00:00 +0000

Sugarscape Model

NetLogo model for in-class exercises.

ODD Protocol

Thu, 22 Aug 2019 00:00:00 +0000

Documents on ODD protocol

Optional supplementary reading for Sept. 1.

The journal article, V. Grimm et al. (2010). “The ODD protocol: A review and first update” Ecological Modeling 221, 2760–68. . https://www.ees4760.jmgilligan.org/files/odd/Grimm_2010_ODD_update.pdf
A Word document that provides a template for writing ODDs : https://www.ees4760.jmgilligan.org/files/odd/Grimm_2010_odd_template.docx
Lists of scientific publications using agent-based and individual-based models that either do or don’t use the ODD protocol (this appeared as Appendix 1 of the Grimm et al. paper):

Butterfly Model ODD

Thu, 22 Aug 2019 00:00:00 +0000

Butterfly Model ODD and Scientific Paper

NetLogo model for in-class exercises.

Netlogo model with Butterfly model ODD on the info page , https://ees4760.jmgilligan.org/models/class_04/butterfly_odd.nlogo

Optional supplementary reading.

G. Pe’er, D. Saltz, and K. Frank, “Virtual Corridors for Conservation Management ,” Conservation Biology, 19, 1997–2003 (2005). https://ees4760.jmgilligan.org/files/reading/Peer-VirtualCorridors-2005.pdf

This is the journal paper that developed and reported the butterfly model.

Mushroom Hunt Model

Thu, 22 Aug 2019 00:00:00 +0000

Mushroom Hunt Model (from Chapter 2)

Download the Basic Mushroom-Hunt Model

Butterfly Models

Thu, 22 Aug 2019 00:00:00 +0000

Butterfly Model for In-Class Exercises on Sept. 3

Download the Basic Butterfly Model
Download the Enhanced Butterfly Model that we wrote in class.

I have made a few changes to the enhanced model that are different from what we did in class:
- I changed the name of the turtles-own variable start-patch to origin to be more concise.
- I changed the equation for the corridor width from $$ \frac{\text{# patches visited}}{\text{sum}(\text{distance-moved})} $$ to $$ \frac{\text{# patches visited}}{\text{mean}(\text{distance-moved})} $$ because that’s what the book uses in Chapter 5.
- I define the turtle to be at the top of a hill when its patch is the highest in a radius of 3 patches, rather than the highest of all its neighbors.
- I add a turtles-own variable at-top? that records whether the turtle is at the top of a hill, and in the to go procedure, I tell the model to stop running if all the turtles are at the top of a hill before it gets to 1000 ticks.

Science with Butterfly Models

Thu, 22 Aug 2019 00:00:00 +0000

Butterfly Model for In-Class Exercises on Sept. 8

A single ZIP file with all the files https://ees4760.jmgilligan.org/models/class_06/class_06.zip

Or individual files

A butterfly model from Chapter 5:
https://ees4760.jmgilligan.org/models/class_06/butterfly_class_06a.nlogo
A version of the butterfly model with modifications:
https://ees4760.jmgilligan.org/models/class_06/butterfly_class_06b.nlogo
Versions of the butterfly model with code for testing:
- https://ees4760.jmgilligan.org/models/class_06/butterfly_class_06c.nlogo
- https://ees4760.jmgilligan.org/models/class_06/butterfly_class_06c_testing.nlogo
A digital elevation map of real hills
https://ees4760.jmgilligan.org/models/class_06/ElevationData.txt

Culture Dissemination Model with Errors

Thu, 22 Aug 2019 00:00:00 +0000

Fixing Errors in Models

Optimizing Butterfly Model for Mating

Fri, 13 Sep 2019 00:00:00 +0000

Updated Butterfly Model

Butterfly model for optimizing q to maximize mating https://ees4760.jmgilligan.org/models/class_07/butterfly_class_7.nlogo
Elevation data for Butterfly model https://ees4760.jmgilligan.org/models/class_07/ElevationData.txt
BehaviorSpace output for optimizing mating for butterflies starting at the edge of the world: https://ees4760.jmgilligan.org/models/class_07/butterfly_class_7%20optimize-mating-table.csv
BehaviorSpace output for optimizing mating for butterflies starting at different locations: https://ees4760.jmgilligan.org/models/class_07/butterfly_class_7%20optimize-mating-big-table.csv

Flocking Model for Studying Emergence

Thu, 22 Aug 2019 00:00:00 +0000

Modified flocking model for stuying emergence

Butterfly Model for Practicing Observations

Thu, 22 Aug 2019 00:00:00 +0000

Modified butterfly model for practicing observations

Link Demonstration Model

Mon, 01 Jan 2018 00:00:00 +0000

Demonstration model for links

Link demo model

Objectives and Adaptations

Thu, 22 Aug 2019 00:00:00 +0000

Modified business-investor model for testing different objectives and decision strategies

Interaction Models

Thu, 03 Oct 2019 00:00:00 +0000

Telemarketer and Prisoner’s Dilemma models for in-class exercises about

interactions

class_14_models.zip , which contains:
- Prisoner’s Dilemma Models
  - PD_simple.nlogo
  - PD_reciprocity.nlogo
- Behaviorspace Output:
  - PD_simple_experiment table.csv
  - PD_reciprocity_experiment table.csv

Team Project Templates

Mon, 01 Jan 2018 00:00:00 +0000

Templates for programming team-project models

Business Investor Model

Printable PDF
Text file that you can paste into the “info” tab in your NetLogo model.
NetLogo template

Telemarketer Model:

Printable PDF
Text file that you can paste into the “info” tab in your NetLogo model.
Figure for ODD
NetLogo template

Models for Scheduling

Thu, 22 Aug 2019 00:00:00 +0000

Models for in-class exercises on scheduling

class_17_models.zip , which contains:
- Mousetrap models:
  - Mousetrap_Ch14_v1.nlogo
    - Discrete events on integer ticks
  - Mousetrap_Ch14_v2.nlogo
    - Semi-discrete events on fractional ticks
  - Mousetrap_Ch14_v3.nlogo
    - Continuous events, tracking balls in air

Breeding Synchrony:
- Ch_23_4_breeding_synchrony.nlogo

Stochasticity: Stochastic Business Investor

Thu, 22 Aug 2019 00:00:00 +0000

Stochastic business-investor model for in-class exercise

class_18_models.zip , which contains:
- Stochastic Business-Investor model:
  - NetLogo model: business_investor_class_18.nlogo

Collectives: Wild-Dog Models

Thu, 22 Aug 2019 00:00:00 +0000

Wild-dog models for in-class exercises on collectives

class_19_models.zip , which contains:
- Wild-dog model:
  - NetLogo model: wild_dogs.nlogo
  - ODD: wild_dog_odd.pdf
- Behaviorspace output:
  - Varying initialization (number and size of packs at beginning): wild_dogs vary_initialization_pe-table.csv
  - Varying disperser pack parameters (meeting rate and mortality): wild_dogs vary_meeting_disp_mortality_pe-table.csv

Theory Development: Wood Hoopoe Model

Thu, 22 Aug 2019 00:00:00 +0000

Wood Hoopoe breeding models for in-class exercises on theory development

class_21_models.zip , which contains:
- Wood Hoopoe model:
  - NetLogo model: wood_hoopoe_class_21.nlogo
  - ODD: wood_hoopoe_odd.pdf
  - NetLogo model with alternate strategies: wood_hoopoe_strategies.nlogo

Calibration and Parameterization

Thu, 22 Aug 2019 00:00:00 +0000

Wood Hoopoe breeding models for in-class exercises on parameterization and calibration

class_22_models.zip , which contains:
- Wood Hoopoe NetLogo model: Sect20-5_WoodHoopoes_2ndEd.nlogo
- R Scripts to analyze behaviorspace output:
  - process_bs.R
  - analyze_woodhoopoe.R
- Behaviorspace output:
  - Sect20-5_WoodHoopoes_2ndEd Calibration-table.csv

Optional reading for Agent-Based Models in Practice

Thu, 22 Aug 2019 00:00:00 +0000

Optional supplementary reading

Analyzing and Understanding Models

Thu, 22 Aug 2019 00:00:00 +0000

Schelling Segregation Model for In-Class Analysis Exercise

class_24_models.zip , which contains:
- Schelling segregation model: segregation.nlogo

Course Description

Thu, 26 Aug 2021 00:00:00 +0000

Printable syllabus

Course Description

Basic Info:

Professor

J. Magnolia Gilligan (they/them/theirs)
Office: SC 5735
Email: j.magnolia.gilligan@vanderbilt.edu
Office Hours: M 10:00–11:00, W 2:00-3:00, or by appointment

Schedule

Class meetings: MW 8:40–9:55, SC 5722

Catalog Description

EES 4760/5760 Agent- and Individual-Based Computational Modeling Applications in natural, social, and behavioral sciences and engineering. Designing, programming, and documenting models. Using models for experiments. Examples from environmental science, ecology, economics, urban planning, and medicine. Familiarity with basic statistics and proficiency in algebra are expected. [3] (MNS)

ODD for Business Investor Model

Thu, 22 Aug 2019 00:00:00 +0000

THE BUSINESS INVESTOR MODEL

This model was produced by S. Railsback and V. Grimm for Chapter 10 of the book Agent-Based and Individual-Based Modeling, 2nd edition (2019).

This is the first version of the model, as described in Section 10.4.1.

OVERVIEW

PURPOSE AND PATTERNS

The primary purpose of this model is to explore the effects of sensing—what information agents have and how they obtain it—on emergent outcomes of a model in which agents make adaptive decisions using sensed information. The model uses investment decisions as an example, but it is not intended to represent any real investment approach or business sector. (In fact, you will see by the end of chapter 12 that models like this one that are designed mainly to explore the system-level effects of sensing and other concepts can produce very different results depending on exactly how those concepts are implemented. What can we learn from such models if their results depend on what seem like details? In part III of this course we will learn to solve this problem by tying models more closely to real systems.)

ODD for Telemarketer Model

Thu, 22 Aug 2019 00:00:00 +0000

THE TELEMARKETER MODEL

This model was produced by S. Railsback and V. Grimm for the book: Agent-based and Individual-Based Modeling: A Practical Introduction, 2nd edition (2019).

This version is the first, basic version of the model as described in Section 13.3.1.

Let us visit the formerly remote land of Wasellya, which has developed very rapidly, so suddenly all its citizens have telephones. Naturally, the “invasion” of telephone technology is followed rapidly by an invasion of people tempted to start a telemarketing business. Is this a good business risk? How many telemarketers will stay in business, for how long? How does the average life span of a telemarketing company depend on how many are started? Here is the ODD description of a simple model for this problem; you should implement the model.

Wed, 19 Apr 2017 00:00:00 +0000

Printable reading assignment sheet

Printable homework assignment sheet

Date	Lesson	Reading	Slides	Assignment
Wednesday, Aug 20, 2025	Introduction
Monday, Aug 25, 2025	The computer modeling cycle
Wednesday, Aug 27, 2025	Introduction to NetLogo
Monday, Sep 1, 2025	Specifying models: The ODD protocol
Wednesday, Sep 3, 2025	Your first model
Monday, Sep 8, 2025	Using models for science
Wednesday, Sep 10, 2025	Testing and validating models
Monday, Sep 15, 2025	Choosing Research Projects
Wednesday, Sep 17, 2025	Emergence
Friday, Sep 19, 2025	Indiv. Project: Research project proposal
Monday, Sep 22, 2025	Observation
Wednesday, Sep 24, 2025	Sensing
Monday, Sep 29, 2025	Adaptive Behavior and Objectives
Wednesday, Oct 1, 2025	Prediction
Monday, Oct 6, 2025	Interaction
Wednesday, Oct 8, 2025	Team Presentations
Monday, Oct 13, 2025	Fall Break
Wednesday, Oct 15, 2025	Research Project ODDs
Friday, Oct 17, 2025	Team Project: Team modeling project report
Monday, Oct 20, 2025	Scheduling
Wednesday, Oct 22, 2025	Stochasticity
Monday, Oct 27, 2025	Collectives
Wednesday, Oct 29, 2025	Patterns
Monday, Nov 3, 2025	Theory Development
Wednesday, Nov 5, 2025	Parameterization and Calibration
Monday, Nov 10, 2025	Agent-Based Models in Practice
Wednesday, Nov 12, 2025	Analyzing ABMs
Monday, Nov 17, 2025	Sensitivity and Robustness
Wednesday, Nov 19, 2025	Looking Ahead: ABMs Beyond this Course
Monday, Nov 24, 2025	Thanksgiving Break
Wednesday, Nov 26, 2025	Thanksgiving Break
Monday, Dec 1, 2025	Presentations
Wednesday, Dec 3, 2025	Presentations
Saturday, Dec 6, 2025	Indiv. Project: Research project report

Policies

Thu, 13 Apr 2017 00:00:00 +0000

Printable syllabus

Assignment policy

I expect you to complete the assigned reading before class on the day for which it is assigned.

Homework will be due by 11:59 PM on the due date. You will turn in homework to Brightspace.

General instructions for reading assignments

Do the assigned reading before you come to class on the date for which it is assigned. If you have questions or find the ideas presented in the readings confusing, I encourage you to ask questions in class.

Mon, 01 Jan 0001 00:00:00 +0000

EES 57650/5760

Modules

Mon, 01 Jan 0001 00:00:00 +0000

Topics: CO2 concentration, Global mean temperature, Sea level rise, Land ice sheet melt, Arctic sea ice cover
Skills: Data wrangling: plain text formats, Tidy data, Data visualization, Smoothing

Topics: Coexistence, Bet Hedging, Limit Cycles, Bifurcations, Deterministic Chaos
Skills: Flow control, functions, iterators, writing R packages, testing, literate documentation

From Worm et al. 2006, https://doi.org/10.1126/science.1132294

Topics: Fisheries, reproducibility, missing data, data visualization and inference
Skills:: Relational databases, SQL

Technologies and data formats: Simple Features Access (ISO 19125) (used in GIS, geojson), Spatial rasters (e.g. geotiff, netcdf), interactive mapping.

From Cerbellos et al., https://doi.org/10.1126/sciadv.1400253

Topics: ICUN Redlist, Fossil record, Taxonomy, Remote and unstructured data
Skills: JSON, curl, REST APIs, regular expressions

Tools

Mon, 01 Jan 0001 00:00:00 +0000

Software Tools for the Course

NetLogo

Get Started!

Explore Published Models

Analyze Behaviorspace Tool

The Analyze Behaviorspace tool can be reached online at https://www.ees4760.jmgilligan.org/analyze_behaviorspace/ , or if you use R , you can install the tool on your own computer by following the instructions at https://github.com/j-magnolia/analyzeBehaviorspace .

R for Statistical Analysis

You do not need to use R for this course, but people who are familiar with R may find that it is a powerful tool for analyzing NetLogo models, and there are tools for integrating NetLogo with R .

EES 4760/5760: Agent- and Individual-Based Computational Modeling on EES 4760/5760

Set up NetLogo

Homework

Preliminary Information

Homework Exercises:

Introducing NetLogo

Homework

Homework Exercises:

The computer modeling cycle

Reading:

Required Reading (everyone):

Optional Extra Reading:

Reading Notes:

Becoming familiar with NetLogo

Homework

Preliminary Information

Homework Exercises:

Introduction to NetLogo

Reading:

Required Reading (everyone):

Optional Extra Reading:

Reading Notes:

Experimenting with NetLogo

Homework

Preliminary Information

Specifying models: The ODD protocol

Reading:

Required Reading (everyone):

Reading Notes:

Science with models: Butterfly mating

Homework

Preliminary Information

Your first model

Reading:

Required Reading (everyone):

Reading Notes:

Reproducing a model from its ODD

Homework

Homework Exercises:

Notes on Homework:

Using models for science

Reading:

Required Reading (everyone):

Optional Extra Reading:

Reading Notes:

Research project proposal

Homework

Homework Exercises:

Notes on Homework:

Testing and validating models

Reading:

Required Reading (everyone):

Reading Notes:

Testing and debugging

Homework

Homework Exercises:

Notes on Homework:

Choosing Research Projects

Reading:

Required Reading (everyone):

Reading Notes:

Analyzing model experiments

Homework

Homework Exercises:

Emergence

Reading:

Required Reading (everyone):

Reading Notes:

Programming agent sensing

Homework

Homework Exercises:

Observation

Reading:

Required Reading (everyone):

Reading Notes:

Resources

Further Reading about Agent-Based Modeling and a Guide to Computational Tools and Resources

Team modeling project presentations

Homework

Homework Exercises: